Performance and intestinal microbiota of chickens receiving probiotic in the feed and submitted to antibiotic therapy

The purpose of this study was to verify the ability of a probiotic in the feed to maintain the stability of the gut microbiota in chickens after antibiotic therapy and its association with growth performance. One thousand six hundred twenty 1‐day‐old Cobb male were housed in floor pens (36 pens, 45 birds/pen) and were fed corn‐/soya bean meal‐based diets supplemented with or without probiotic (Bacillus subtilis) during the entire rearing phase. From 21 to 24 days of age (three consecutive days), the chickens were submitted to antibiotic therapy via drinking water (bacitracin and neomycin) in order to mimic a field treatment and induce dysbiosis. Growth performance was monitored until 42 days of age. At 2, 4 and 6 days after antibiotic therapy, three chickens from each pen were euthanized and the contents of the small intestine and caeca were collected and pooled. The trial was conducted with four treatments and nine replicates in a 2 × 2 factorial arrangement for performance characteristics (with and without probiotic × with and without antibiotic therapy); for the intestinal microbiota, it was in a 2 × 2 × 3 factorial arrangement (with and without probiotic × with and without antibiotic therapy × 2, 4 and 6 days after the antibiotic therapy) with three replicates per treatment. Terminal restriction length polymorphism (T‐RFLP) analysis showed that the structure of gut bacterial community was shaped by the intestinal segment and by the time after the antibiotic therapy. The number of 16S rDNAs copies in caecum contents decreased with time after the therapeutic treatment. The antibiotic therapy and dietary probiotic supplementation decreased richness and diversity indexes in the caecal contents. The improved performance observed in birds supplemented with probiotic may be related to changes promoted by the feed additive in the structure of the intestinal bacterial communities and phylogenetic groups. Antibiotic therapy modified the bacterial structure, but did not cause loss of broiler performance.     

基于高通量测序的不同填闲作物对黄瓜连作土壤微生物群落结构的影响

以连作3 a黄瓜的日光温室土壤为研究对象,以黄瓜为主栽作物,分别以大葱、普通白菜和小麦为冬夏季休闲期的填闲作物,采用高通量测序技术分析不同填闲模式对黄瓜连作土壤微生物群落结构的影响。结果表明:3种填闲模式处理的土壤细菌群落和真菌群落中的主要物种基本一致,但是相对丰度存在差异。在细菌属水平上,填闲小麦处理中Flexibacter、Nitrosomonadaceae_uncultured、Anaerolineaceae_unculture的相对丰度显著低于填闲大葱和普通白菜,而Flavobacterium、Clostridium、Peptostreptococcaceae_incertae_sedis的相对丰度显著高于填闲大葱和普通白菜;在真菌属水平上,填闲小麦处理中Ascomycota_unclassified、Hypocreales_unclassified、Humicola的相对丰度显著低于填闲大葱和普通白菜,而Fusarium、Pyrenochaeta、Nectriaceae_unclassified、Preussia的相对丰度显著高于填闲大葱和普通白菜。说明不同填闲作物对土壤微生物群落结构和多样性的影响存在差异。     

The impact of rumen cannulation on the microbial community of goat rumens as measured using 16S rRNA high‐throughput sequencing

The main objective of this study was to determine the impact of rumen cannulation on the microbial community of goat rumens using 16S rRNA high‐throughput sequencing. Twelve Boer crossbred goats were used in the experiment: six goats were surgically fitted with rumen cannula, and the other six were used as controls. All goats were fed the same diet for 20 days, after which their rumen digesta were sampled once per week for three consecutive weeks. Total microbial DNA was extracted from the collected rumen fluid and was used as a template to amplify the V4 hypervariable region of the 16S rRNA gene. High‐throughput sequencing was performed using an Illumina MiSeq platform, and the sequences were analyzed primarily using the Quantitative Insights into Microbial Ecology pipeline software. The results showed that the Chao 1 index, the observed species index and the Shannon‐Wiener index were not significantly different (p > 0.05) between the two groups. Bacteroidetes, Firmicutes, Tenericutes were the predominant phylum in both groups, and their relative abundance was 60.63%, 29.48%, 2.24% (n = 6, CT group) and 61.17%, 26.92%, 1.66% (n = 6, RC group) respectively. At the phylum level, the relative abundance of Proteobacteria was significantly higher (p < 0.001) in the microbial communities of RC goats, and Planctomycetes and Chloroflexi were significantly lower (p = 0.02). The abundances of other phyla were not significantly different between treatments. A total of 19 lower‐level taxa also exhibited significant differences (p < 0.05) in relative abundance between the groups. In addition, there were 18 genera shared within the control group, 26 shared within the rumen‐cannulated group, and 16 shared by both groups. Prevotella was the most abundant shared genus, although its abundance was not significantly different (p > 0.05) between the groups. In conclusion, although the most abundant microbes kept stable, rumen cannulation had the potential to significantly change rumen microbial communities in goats.     

摩拉水牛和尼里-拉菲水牛PRKAA2基因SNPs检测及遗传多样性分析

为研究水牛蛋白激酶AMP活化的催化亚基α2（protein kinase AMP-activated catalytic subunit alpha 2,PRKAA2）基因多态性,本试验以摩拉水牛和尼里-拉菲水牛基因组DNA为模板,扩增PRKAA2基因外显子4及内含子3部分序列,通过常规测序法检测其SNP并进行遗传多样性分析。结果发现,PRKAA2基因外显子4内存在1个SNP位点（c.462 G>A）,PRKAA2基因内含子3部分序列存在3个SNPs位点（IVS3.557 T>C、IVS3.560 C>T和IVS3.565 G>A）。经遗传多样性分析表明,在c.462 G>A位点的野生纯合型和杂合型比突变纯合型更有优势,IVS3.557 T>C和IVS3.560 C>T位点的突变纯合型为非优势基因型,IVS3.565 G>A位点杂合型为优势基因型。IVS3.565 G>A位点在摩拉水牛群体中处于Hardy-Weinberg非平衡状态;c.462 G>A位点在尼里-拉菲水牛群体中处于Hardy-Weinberg非平衡状态。4个SNPs位点在摩拉水牛群体中均为中度多态;c.462 G>A、IVS3.557 T>C位点在尼里-拉菲水牛群体中为低度多态,IVS3.560 C>T、IVS3.565 G>A位点为中度多态。IVS3.557 T>C位点在两个水牛群体中杂合度较低。说明摩拉水牛IVS3.565 G>A位点和尼里-拉菲水牛c.462 G>A位点的基因型频率和基因频率遗传状态不平衡,尼里-拉菲水牛群体中IVS3.557 T>C位点遗传变异小,选择潜力不高。4个多态位点可以构建5种单倍型,其中T-C-G-G是摩拉水牛群体和尼里-拉菲水牛群体的优势单倍型。综上,本研究检测的摩拉水牛和尼里-拉菲水牛PRKAA2基因上4个SNPs位点可为水牛标记辅助选择育种提供参考。     

犬源复合益生菌对脾气虚犬盲肠菌群的影响

本试验旨在通过高通量测序技术研究犬源复合益生菌对脾气虚犬盲肠菌群的影响。选取24只1岁龄比格犬,随机分成4组:对照组、脾气虚组、自然恢复组和益生菌治疗组,每组6只。其中,对照组饲喂基础饲粮;脾气虚组、自然恢复组和益生菌治疗组在饲喂基础饲粮的同时每天按照10 mL/kg BW的剂量灌喂番泻叶水煎液,连续灌喂7 d,建立脾气虚模型。在试验第7天,采集脾气虚组犬盲肠内容物;对照组和自然恢复组犬继续饲喂基础饲粮7 d,益生菌治疗组犬在饲喂基础饲粮的基础上每天按照1×10~9CFU/只的剂量灌服犬源复合益生菌7 d。在试验第14天,随机从对照组、自然恢复组和益生菌治疗组各选4只犬采集盲肠内容物。利用Illumina HiSeq 2500平台及QIIME测序软件对各组犬盲肠内容物进行生物信息学分析。结果显示:1)对照组与益生菌治疗组盲肠菌群的ACE指数、Chao1指数、Shannon指数均高于脾气虚组与自然恢复组,而Simpson指数则低于脾气虚组与自然恢复组。2)益生菌治疗组盲肠菌群中拟杆菌门、纲、目、科以及芽孢杆菌纲、属的相对丰度均显著高于对照组和脾气虚组(P<0.05),其他菌群在不同分类水平上的相对丰度均与对照组无显著差异(P>0.05)。综上所述,犬源复合益生菌不仅能够使番泻叶诱导的脾气虚犬盲肠菌群多样性恢复至正常犬水平,而且还能够提高盲肠菌群中有益菌拟杆菌、芽孢杆菌的占比,对脾气虚犬盲肠菌群结构有良好的调节作用。     

血清4型鸡腺病毒AHHN分离株全基因组测序及其致病性研究

为明确一株I群C亚群鸡腺病毒血清4型(FAdV-4)AHHN分离株基因组特征及其致病性,本研究对该病毒的全基因组序列进行测定,结果显示:AHHN分离株的基因组全长为43723bp,G+C含量为54.87%,ORF29序列具有FAdV-4变异株29aa缺失的特征。0.1mL/羽(1×10^5TCID50)病毒量肌肉注射3周龄SPF鸡2d后,感染鸡出现急性感染症状,5d内全部死亡;剖检可见其肝脏变黄,表面大量出血灶,伴有心包积液、胸腺萎缩、法氏囊萎缩等眼观病变;病理组织学观察显示,感染鸡肝脏呈现典型的嗜碱性包涵体肝炎病变;病毒载量测定结果显示,各脏器均有不同程度的病毒复制。上述结果表明,FAdV-4AHHN分离株对鸡具有高致病性及广泛的组织嗜性。本研究为进一步研究FAdV-4功能基因对病毒毒力的影响奠定了基础。     

增强子预测及靶向测序技术研究进展

增强子在传统上被定义为不依赖转录方向及与目标启动子的相对位置来调控一个或多个基因转录的基因组顺式调控序列,其活性对生长发育、基因表达多样性、进化及人类疾病发生起到关键的调控作用,因此,了解增强子的功能特性不仅有利于理解基因表达的时空特异性,也有助于最终揭示细胞分化、物种进化及非编码区域变异导致疾病等关键的生物学问题。随着高通量测序技术的快速发展,增强子的预测鉴定、识别及功能注释的方法和工具也呈现出多样性,包括序列基序分析、转录因子和辅因子的体内结合位点、特征染色质和组蛋白修饰、大规模并行增强子分析,以及CRISPR(clustered regularly interspaced short palindromic repeats)相关技术。文章就高通量测序技术在全基因组水平上利用调节因子结合位点、染色质可接近性、组蛋白修饰、增强子与启动子的相互作用、增强子RNAs(eRNAs)和体外荧光素酶等技术对增强子鉴定、识别、预测的6种方法进行了综述,并就如何利用基因编辑技术靶向研究增强子进行了详细阐述,最后展望了全基因组水平上的增强子研究和个体研究增强子的作用,并详细描述了靶向预测增强子的方法,比较了每种方法的优势和局限性,为深入开展该领域的研究工作提供参考。     

番石榴结合态多酚对小鼠肠道菌群结构及多样性的影响研究

为探究番石榴结合态多酚对小鼠肠道菌群的影响,本试验将CD-1小鼠分为空白组、高浓度组(500 mg·kg^-1)和低浓度组(100 mg·kg^-1)3组,在灌胃5周后,收集小鼠的无菌粪便,扩增肠道菌群16S rRNA基因高变域V3-V4,通过16S rRNA基因扩增子测序技术检测小鼠肠道菌群的α多样性、β多样性,以及门、属水平的物种组成。结果表明,与空白组相比,低浓度组中菌群的均匀性和丰富度显著提高(P<0.05);基于门水平分析,厚壁菌门、拟杆菌门和疣微菌门3个菌门的相对丰度值较大;在属水平中,高低浓度组均能降低拟杆菌属相对丰度,低浓度组能提高乳杆菌相对丰度,并且高浓度组中艾克曼菌属的相对丰度大幅提高。综上所述,番石榴结合态多酚能提高小鼠肠道菌群的均匀性和丰富度,且对菌群结构具有调节作用,既能提高益生菌的相对丰度,也能降低有害菌的相对丰度。本研究结果可为番石榴结合态多酚的活性研究和实际应用提供理论参考。